NOL11

protein-coding

nucleolar protein 11, the group of UTPa subcomplex|Small nucleolar RNA protein coding host genes

Gene summary

Enables RNA binding activity. Involved in maturation of SSU-rRNA and positive regulation of transcription of nucleolar large rRNA by RNA polymerase I. Located in nucleolus. Part of t-UTP complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_015462.5

Inheritance

—

ClinVar variants

U:99B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.44

Max pathogenic AF

—

Genomic locus

chr17:67,717,931-67,744,531

External References & Databases

Ensembl (ENSG00000130935)

Transcript & Mutation Effects

hg38 • Region Span ~26.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NOL11 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 101

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015462.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			99 clinvar	7 clinvar	1 clinvar	107
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	99	7	2	108

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015462.5	RefSeq	NP_056277.2	18	MANE Select
ENST00000253247.9	Ensembl	ENSP00000253247.4	18	MANE Select
NM_001303272.2	RefSeq	NP_001290201.1	13	Standard
ENST00000580833.1	Ensembl	ENSP00000464015.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

rRNA processing
Metabolism of RNA
rRNA modification in the nucleus and cytosol
rRNA processing in the nucleus and cytosol

Biological Process

rRNA processing
maturation of SSU-rRNA
positive regulation of transcription of nucleolar large rRNA by RNA polymerase I

Molecular Function

RNA binding
protein binding

Cellular Component

nucleoplasm
nucleolus
t-UTP complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000253247
Coding exons: 18
Length: 26699
Individuals with no LoFs: 125704
Homozygous LoFs: 0
Heterozygous LoFs: 44
Defined: 125748
p: 0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.416	340	362	0.938	0.0000179	4683
Missense (PolyPhen)		68	86.682	0.78448		1252
Synonymous	-0.482	138	131	1.05	0.00000671	1347
Loss of Function	3.26	17	38.9	0.437	0.00000181	520

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00027	0.00018	rare
Latino/Admixed American	0.000033	0.000029	rare
Ashkenazi Jewish	0.00041	0.00040	rare
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00024	0.00024	rare
South Asian	0.00014	0.00013	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Ribosome biogenesis factor. May be required for both optimal rDNA transcription and small subunit (SSU) pre-rRNA processing at sites A', A0, 1 and 2b. {ECO:0000269|PubMed:22916032}.;

Recessive Scores

pRec: 0.0798

Intolerance Scores

LoFtool: 0.792
RVIS EVS: 0.29
RVIS percentile EVS: 71.57

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.737

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium